Australian national carrier Qantas resumed operations on Monday after the dramatic escalation of its dispute with unions led to an unprecedented 44-hour grounding leaving thousands of its passengers stranded.

The first Qantas domestic flight took off from the airport in Melbourne with passengers cheering as boarding began after the airline was grounded on Saturday following series of union issues.

According to the local media, cheers were heard at gate two of the domestic terminal as the final boarding call was made for QF 438 to Sydney.

Passengers started boarding flights in Melbourne after the Civil Aviation Safety Authority granted the airline approval to fly.

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Flights to Brisbane, Canberra and Perth are also ready to fly. However, many other passengers were still facing delays.

Meanwhile, flight QF46 from Christchurch, the first international Qantas flight to land in Sydney, has touched down and passengers have disembarked.

However the airline will not by fully operational before Wednesday, with the initial focus being on the busy Sydney-Melbourne route, reports said.

The resumption of flights was ordered by industrial regulator Fair Work Australia, which after a marathon hearing ordered a complete end to the dispute between Qantas and unions.

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Justice Geoffrey Giudice, part of the industrial umpire panel, said the decision allowed for further negotiations between Qantas and unions over the next 21 days to try and hammer out their differences.

Qantas chief Alan Joyce while talking to reporters earlier in Sydney said, "All industrial action is now over and we have certainty," and added, "We will be returning to business as usual over the next 24 hours."

Head of maintenance operations at Qantas Alan Milne said 22,000 international passengers were stranded offshore, but it hoped the backlog would be cleared by Tuesday.

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Meanwhile, the union representing Qantas baggage handlers and ground crew said it was considering appealing the decision to halt industrial action.

"We are also considering with our legal advisers whether we should appeal this decision," Transport Workers Union (TWU) national secretary Tony Sheldon was quoted as saying in the "Sky News" report.

However, Sheldon said the union wouldn't take action for the next three weeks as long as Qantas acted in good faith.

Meanwhile, pilots expressed concern that Qantas would use upcoming negotiations to "stonewall" employees.

Australian International Pilots Association (AIPA) vice-president Captain Richard Woodward said he predicted the forthcoming negotiations with Qantas would result in a forced arbitration.